In Endless Space, trade routes are set up automatically once a new planet is available to trade with: you're at peace with a race and explore a new planet among that peaceful race, or you become at peace with a race that you were previously in Cold War with.
How does Endless Space decide which of your systems gets the new trade route, if multiple systems qualify for it? If one system's trading capabilities change, by building a new system improvement to give +20% trading effects, or assigning a hero who's good at trading, can that system steal trade routes from other systems in your empire? If you have a system that's fantastic at trading (lots of improvements, huge population and economy, etc.), but has used up all of its available trade routes, and you build an improvement that grants an additional trade route, will it steal a route from one of your less-trade-y systems and thus make you fantastically rich?
Best Answer
From what I've seen during play, your best system will trade with their best system. From there it works its way down until you run out of available systems, or they do.
When you add a new possible trade route or improve the trade bonus on a system, the game re-calculates the trade network. This means your systems can "steal" trade from a "lesser" system in your empire in the trade network.